Pokémon Ebony Version
by Ventus Cherrygarden
Summary: Join Aaron, separated from his sister as he ventures through the Hoenn and Isshu regions! And the original PokéDex holders make their own appearances along the journey!
1. Hoenn: Chapter 000

Chapter 000:

Separation

* * *

Vermilion City (Late Night)

* * *

"C'mon! Move it!" the Rocket Grunt ordered me, pushing me on a ship. The SS Anne to be exact. If only I could reach my Pokéballs...Charmeleon could untie us all.

"Aaron!" My fourteen year old sister called from behind me, also tied up. I turned around and she looked at me with her bright green eyes.

"Hey, these two seem to be related!" Another Grunt called out.

"Oh?" A man dressed in a red and black jacket with dark red hair chimed in.

"Yes sir!" the Grunt saluted.

"The girl goes to Sinnoh." The red head said, pointing to the other boat.

"No! She comes with me!" I yelled, kicking the Grunt away from me.

The red haired man sighed and snapped his fingers. A pack of Houndoom ran in front of me, ready to attack. I growled.

"It's either this way or the hard way." The man said.

"Yeah!" A Grunt added.

I'm tied up...there's nothing I can do...sorry Amelia...I fell to my knees and closed my eyes, letting the Team Rocket members stuff me on the boat to the Hoenn region. This all started when Amelia and I were walking from Celadon to Vermilion. The Team Rocket members ambushed us and tied us up...why us though?


	2. Hoenn: Chapter 001

Chapter 001:

Lost Within

* * *

Sootopolis City Gym (Early Morning)

* * *

"Lord Silver. The boy has been transported." A green-haired girl informed. She wore a a black and red cloak with an "R" emblem across the chest area. Looking up at Silver with bright, blue eyes, she turned to walk out.

"Why thank you, Sgt. Tsuki." Silver said, no emotion in his voice. He stood up as he looked around the Sootopolis Gym.

"_I guess this will have to serve as a base for now..." _He thought.

"Hey! Lemme down from here!" A tied up Trainer yelled.

"Shut up." Silver said coldly and reached for a Pokéball. "Go." Silver mumbled and tossed his Pokéball into the air. His Feraligatr stood tall in front of him. "Ice Beam. Now." Silver ordered. The Feraligatr took in a deep breath and spit a cold rush of wind at the Trainer, freezing him solid.

"A bit harsh, don't you think?" A male voice called from behind him.

"Wanna end up like this Trainer? If not, I suggest you get quiet." Silver ordered.

The sound of a Pokéball being opened was heard.

"You think that's supposed to scare me?" Silver said unemotionally.

A black Charizard approached Silver from behind.

"It should at least make you scared." The male said.

"The shiny Charizard? If it wasn't for those idiots at Research and Development, you wouldn't have that." Silver retorted.

"Whatever. I care nothing for this organization, you know what I'm in it for." The Charizard wielder said bluntly.

"Ah, yes...Project Black..."

* * *

Slateport City (Early Morning)

* * *

I woke up to be on the shores of the Slateport Beach. How did I get here...? I reached for my Pokéballs...wait...one's missing! I panicked and began tossing sand around, aimlessly looking for the Pokéball. Oh no...not Charmeleon...

"Is this yours?" A voice called from behind me.

I looked up to see a male, he looked about my age, maybe a bit older. His hair was pitch-black but he had a blue streak in it. He wore a closed blue and black jacket with a design of a Pokéball in the middle.

"How pathetic. You lost your own Pokéball. Your starter Pokémon at that." The guy said, throwing my Pokéball at me.

I said nothing and stood to my feet.

"Your name?" He demanded.

"Aaron. Aaron Nightingale." I quickly replied.

"The name's Joshua Flyheight." Joshua introduced.

"Where are you from?" I asked.

"Sunyshore City, in Sinnoh." He replied.

"I'm from Fuchsia City."

"All the way from Kanto, hm?" He said surprisingly.

"...yeah...it was kind of a quick trip." I trailed off.

"Me. You. Pokémon battle." Joshua suddenly said.

"Um...er...sure..." I said unwillingly.

"Good. I have four Pokémon." He explained.

"I only have three."

"You'll just have to manage." Joshua replied, laughing.

I grinned. "Well, I can manage with my team."

"Alright then!" He exclaimed, tossing up a Pokéball.

A Luxio excitedly came out, growling.

"Easy now, Luxio." Joshua said calmly.

"Go! Charmeleon!" I yelled, tossing its Pokéball out.

Charmeleon stood by my side, ready for battle.

Fire VS Electric...how can I manage? I couldn't use Pidgeotto...and...'it' won't obey me...

"Luxio, use Shock Wave!" Joshua commanded.

Luxio began charging electricity in its tail and fired it at Charmeleon.

"Dodge and counter with Flamethrower!" I ordered.

Charmeleon quickly dodged and spit out a rush of fire at Luxio.

"Luxio!" Joshua yelled as Luxio was hit by the flames.

Luxio purred and stood its feet.

It's not done yet? Well then...

"Volt Tackle." Joshua said calmly.

Yellow charges of electricity began to form around Luxio's body.

V-Volt Tackle! It's over...

Luxio roared and charged at Charmeleon.

"Charmeleon!" I yelled.

Charmeleon was tackled to ground, electric charges faintly emanating from his body.

"Return..." I said, returning Charmeleon to his Pokéball.

"Good job, Luxio." Joshua praised, returning Luxio to its Pokéball.

"What Pokémon do you have anyway?" He asked.

"Charmeleon, Pidgeotto, and...Mewtwo..." I uttered.

"...M-Mewtwo! But how...!" Joshua exclaimed.

"I'm...holding it for someone." I lied through my teeth.

"Don't tell me...were you involved with C-13 Incident?" He asked fearfully.

I stayed silent. The C-13 Incident was an explosion at the Cerulean Cave, nearly destroying the Kanto region. It was said the PokéDex holders Red and Gold perished in the explosion.

Joshua grabbed me by the collar. "Were you! Two Trainers were killed in that explosion! Now tell me! Were you involved!"

I grabbed Joshua's hand and tossed it aside. "No. But I was there."

"Oh..." He said remorsefully.

"Yeah. I'll be on my way now." I said bluntly.

"Hey wait..."

"What?"

"To compensate for just now, I'd like to travel with you." Joshua requested.

"Sure. I haven't been in Hoenn since I was a child, I'd probably need to someone to hang with anyway." I said, laughing. I walked over to the water to see my reflection. My green eyes reflected off the sun while my pitch-black hair was messy as always. I looked up to see a boat sailing towards us.

"Hey Josh..." I said pointing towards a boat. An old man was in the front with a Wingull beside him, flying ahead of the boat.

"Way ahead of you..."

"I think we need to go to Littleroot Town first. To Professor Birch's lab." I explained.

"If that's the case, then we need to travel back through Petalburg. Then Oldale and go south from there."

Josh added.

"Right."

The boat approached us quickly.

"Watch it!" I exclaimed jumping out of the way.

"Yeah!" Joshua said, doing the same.

The boat docked in front of us, and an elderly man stepped off. He was bald and he wore a black robe, and he had white hair on his face. The Wingull landed on his shoulder.

"'Ello!" The man greeted us.

"Hello." Josh and I said.

"The name's Mr. Briney and I sail boats." He explained.

I can see that...

"Well, me and my friend here are looking for a trip back to Petalburg City. And you have a boat...but we'll pay you." Joshua quickly explained.

"No no, I don't charge. There were these three Trainers that helped me in the past. I can't quite remember their names though...but either way, I will take you back to Petalburg!" Mr. Briney agreed.

"Yes!" Josh and I exclaimed as we ran onto the boat. Mr. Briney and his Wingull followed behind. The elderly man started up the boat. Onto Littleroot Town then...


	3. Hoenn: Chapter 002

Chapter 002:

Childhood Friends

* * *

Route 107 (Mid-Afternoon)

* * *

I yawned and looked up as we sailed on the smooth waters. It feels like we've been on the water for hours...I wonder how Amelia is...I sighed.

"Something wrong?" Joshua asked, playing with this odd device on his wrist.

"Nah. Hey, what's that on your wrist?" I asked curiously.

"A Pokétch. They're all the rage in Sinnoh." He replied.

"Ah. I used to have a PokéNav...and a PokéGear. But they broke, so yeah." I informed.

"Land ho!" Mr. Briney suddenly yelled out.

My eyes couldn't believe what they were seeing. A small island, with a Pokémon Gym, Pokémon Center and Mart along with a few houses.

"Petalburg sure has changed..." Joshua muttured.

"This isn't Petalburg City. We're in Dewford Town." I said with annoyance in my voice.

"How right you are, Aaron." Mr. Briney said, docking the ship on the small wooden port. "I hope you don't mind this detour, I have to collect supplies and such. Who knows, you two could get your Badges."

"It's fine, sir." Joshua replied.

"I wanna explore the Granite Cave." I said, pointing at the cave entrance in the far distance. "Maybe I'll find an Aron."

"Like the one that evolves into Larion? Then Aggron?" Josh asked excitedly.

I nodded. "I've always wanted one."

* * *

Dewford Town (Mid-Afternoon)

* * *

"Well then, you two, go on and explore. I'll be done shopping by the time you're done exploring." Mr. Briney explained, walking off the boat towards the Poké Mart.

I got off the boat, only to fall into the sand.

"Ouch." A voice called above me.

I stood up, brushing sand off my clothing.

"Did I trip you?" A male asked. I looked at him. He was exactly my height, spiked green hair with blue eyes. His clothes were...odd. He wore a black leather jacket with the pants to match along with a white bag on his back.

"Yes. You did." Josh chimed in angrily.

The male didn't address him back.

"Excuse my friend here. But yes, you tripped me." I said calmly. Just who was this guy anyway?

"Ah. Well my apologies. Your name?" He asked.

"Aaron Nightingale. Yours?" I introduced.

"Edward, just Edward." He replied. "A pleasure meeting you, Aaron Nightingale." Then, he turned off, walking towards the Granite Cave.

"That was weird...he didn't even acknowledge you..." I mumbled.

"Edward's also from Sinnoh. We grew up together. Except he went onto the League, whereas I didn't." Joshua said, clenching his fist.

"What happened?" I asked.

"Nothing...just c'mon." He said quickly, walking towards the cave.

I wanna know more about this backstory...I'll just see what happens here. I followed behind him. We entered the cave, but it was pitch-black dark.

* * *

Granite Cave (Mid-Afternoon)

* * *

"I see he didn't have the courtesy to use Flash..." Josh grimaced. "Go! Luxio!" He commanded, letting Luxio out of its Pokéball. It purred. "Use Flash!" He commanded again.

Luxio let out a ray of light from its tail, illuminating the darkened cavern. "Thanks Luxio. You can return now." Joshua said calmly, rubbing Luxio's head, then returning it to its Pokéball. We began to trek through the cave, we then approached a ladder.

"There's another floor?" Joshua asked curiously.

"Well of course. This ladder goes underground, stretching under the sea floor." I elaborated, climbing down the ladder. Josh followed.

The second floor was cooler than the first one. I examined our surroundings, and I saw a hole in the cavern wall.

"Hey look!" I exclaimed, pointing at the hole.

"What? It's only a hole in the wall." He replied unenthusiastically.

I shrugged my shoulders and towards the wall, only to be stopped by an angry looking Aron. It glared at me with it's light blue eyes.

"It wants a battle..." I said, grinning, reaching for my Pokéball. "Go! Charmeleon!" I said, throwing the capsule out, releasing the Pokémon inside. Charmeleon let out a growl of excitement. Aron's hardened skin began to glow a bright silver color.

That must be Iron Defense...

I grinned again.

"Use Flamethrower!" I commanded. Charmeleon spit out a rush of fire at the Aron, but it stood still, hardly phased.

"Remember, they have defense." A familiar voice called from behind me, but it wasn't Josh. It was Edward.

"What are YOU doing here!" Joshua exclaimed angrily as he stood beside me, turned around.

Once again, Edward ignored him.

"Josh, chill." I said calmly as Charmeleon used another Flamethrower, doing massive damage on the Aron.

Joshua let out a growl.

"You should catch it before it faints." Edward suggested.

"We don't need your suggestions, prick." Joshua chimed in again.

This time, Edward looked at him. "Listen here, you. Speak when spoken to. And last time I checked, I was talking to Aaron." He said bluntly.

"Who cares?" Josh retaliated.

"You were always the angry type..." Edward trailed off, wiping dirt off of his jacket.

"Shut it!" Josh yelled.

"Exactly." Edward said cooly.

As they argued, I reached in my bag for a Pokéball and tossed it at the nearly fainted Aron.

"Good job." Edward praised. "You have potential, unlike Joshua over here." He added and then walked off into the hole in the wall.

I looked at Josh, he was growling with rage.

"Calm down. Don't let him get to you." I said, attempting to calm him down.

"Fine..." He finally gave in.

"Now, onto the hole in the wall." I suggested, walking into the wall. He followed behind.

In this room of the cavern, there were computers and pieces of technology everywhere.

This must be a laboratory.

Suddenly, I heard an explosion from above.

"The cave's about to collapse!" I yelled, running towards the exit. Joshua followed behind.

Pieces of rock began falling, crushing the computers. A tremor began to occur, shaking the ground. I fell to the ground, nearly being crushed by a rock.

"Go! Pidgeotto!" I yelled, releasing Pidgeotto. I jumped on its back and signaled to Joshua. He climbed on. Pidgeotto spread its wings, knocking a few rock out of the way and began to fly to the sandy beaches of Dewford Town. I looked down at Granite Cave, which is now a gaping hole in the ground. Water began flooding it.

"This is Edward's doing..." Josh murmured as we landed. The citizens of Dewford Town were gathered around, looking as the cave fell in.

"It couldn't be..." I defended.

"...no comment." Joshua said, annoyed.

"Pidgeotto, return." I commanded, returning it to the Pokéball as we got off.

Mr. Briney ran toward us, his Wingull beside him. "Are you two lads okay?" He asked with concern in his voice.

The crowd murmured in talk of the tremor that just occurred.

"We're fine..." I said.

"Well then, ready to head to Petalburg?" He asked anxiously.

"Just like that? You don't wanna find out what happened...?" I asked with confusion in my voice.

"We'll return once you two run your errand." He assured.

Josh and I nodded in agreement and boarded the boat. Mr. Briney started it up and we sailed off, just in time for the sun to begin setting.

* * *

Sootopolis City Gym (Late Night)

* * *

"You didn't complete your mission." Silver said with a slight hint of anger in his voice.

"My apologies, sir...I just...ran into an old friend..." A teenage male said, standing in the dark.

"Unacceptable. But, I'll have to let it slide." Silver said coldly.

"Oh give him a break." A girl chimed in, also in the dark.

"And who asked you?" Silver said, directing his comment toward the girl.

"Speak unless spoken to." The male added.

The girl stayed silent. The air within the Sootopolis Gym got colder as the room got silent.


	4. Hoenn: Chapter 003

Chapter 003:

Ghost

Mr. Briney's Cottage (Late Night)

"Gonna finish that rice cake?" Joshua asked greedily, his hand reaching for my half-eaten rice cake in front of me. Charmeleon then instinctively snatched it before he could get to it, gulping it down in one bite. I wanted that rice cake. Badly. I stayed silent while Josh and Charmeleon bickered and argued over food. Mr. Briney, the kind-hearted elderly man who sailed us here, was in the kitchen, mixing something in a pot.

"...hey...I wanted that rice cake!" I said, losing my train of thought. Joshua and Charmeleon suddenly stopped arguing and began glaring at me. "What! I wanted it!" I exclaimed.

Charmeleon then jumped on me playfully, and I began laughing. Luxio popped out of its Pokéball and assisted Charmeleon in showing me affection.

"Hmph. Pokémon aren't meant as companions. Only tools of destruction." A voice called from the door. The voice sounded...odd, as if multiple were speaking, in a distorted harmony. We all looked up to see a figure, about my height, cloaked with a hooded robe, standing there. I stood and approached the figure, Charmeleon beside me, growling aggressively. "And you are?" I asked calmly.

"Me? I'm a figment of your imagination, an illusion." The figure replied to me. I could hear footsteps approaching behind me, it was Joshua. "A figment of his imagination? Then how come I can see you?" Josh challenged. "You think you can see me, when really, I'm not here." He replied.

"This makes no sense." I said, readying to command Charmeleon. The figure then turned its back and walked out towards the towering trees of the Petalburg Woods. "Should we follow?" Joshua asked. "No, let's just head out." I quickly suggested. But then, I turned around to see Mr. Briney missing. "What the...? Where'd he go off to!" Josh exclaimed. "He must've went out the back door to go outside." I clarified, "He WAS making something in that pot, probably out for more Berries."

We called our Pokémon back and we walked outside.

Route 104 (Late Night)

"It's dark out here..." Joshua complained. "Get over it." I replied. "Gah, whatever." He replied. We walked for about five minutes or so, then, Petalburg City was in my sight. "One city down...one more to go." I mumbled.

Petalburg City (Late Night)

"I'm sorry, but the Petalburg Gym is closed right now." A woman explained to a young Trainer. The woman was a bit taller than me. She had long brown hair that was worn down. A red bandana with a Pokéball symbol on it covered a part of her head. Her eyes were a golden brown looking color, her shirt was red as well. Lastly, she had a white skirt with short, black leggings under it and a yellow bag on her back with red and yellow shoes. Joshua was in awe, gazing at her.

"Snap out of it, will ya'? You must not realize who that is." I said with annoyance in my voice. "Who is it?" Josh asked, still staring at her. "That's Sapphire, one of the PokéDex Holders. Her and Ruby, another one, are um...dating." I explained. The Trainer that Sapphire was talking to stormed off in anger. She then turned to see us. "...and oh yeah, she's friends with my younger sister..." I grimaced.

"Aaron!" Sapphire exclaimed, running towards me. She then embraced me in a hug, squeezing me tightly. I could tell Joshua was having a fit on the inside.

"H-hello Sapphire..." I wheezed as she hugged me. I couldn't breathe...

"How've you been?" She said with a smile, letting me go. Joshua was going through his bag to hide himself.

"I've been...fine, you could say." I lied through my teeth. I lost my sister, literally. Not the best of times.

"Good to hear. Who's your friend?" Sapphire asked curiously.

"This right here..." I started, grabbing Joshua by the shirt, "is Joshua Flyheight. A fellow Pokémon Trainer."

"H-hi." Josh stuttered.

"Hello." Sapphire said warmly. "So where are you two headed?"

"Littleroot Town. We started at Slateport City." I explained.

"Aaron, aren't you from Kanto?" She asked, raising her eyebrow.

"Heh...yeah, don't ask how I got to Slateport." I advised.

"It's not because of that incident is it?" Sapphire questioned.

"More than likely..." I mumbled.

"Then, Amelia must've been dragged into it..." Worry filled her eyes as she said those words.

I stayed silent. That was the truth...because of a request to hold dangerous contraband, my little sister was kidnapped and separated from me.

"You wish to find your sister?" A voice called from behind us. The same, distorted voice from earlier. The three of quickly turned around, grabbing our Pokéballs, ready to use if needed. There it was. The same hooded figure.

"Who are you and what do you want!" Joshua snapped at the figure.

"Me? I'm just here to assist Mr. Nightingale here." The figure said calmly.

"Really now? Assist me with what exactly?" I asked curiously.

"Keeping that secret of yours...a secret." The figure replied knowingly.

My eyes widened and stood in shock. "W-who exactly a-are you?" I staggered.

"I go by the name of G. I have intel on just about everyone in the world. And every organization." G explained, letting out a chuckle.

Sapphire stayed silent the whole time.

"Something wrong, Sapphire?" G asked, making his comment directly to her.

"Not at all." She said calmly. I could tell something was wrong.

"Well, I'll be on my way. It was a pleasure meeting the infamous Aaron Nightingale in person." He said, taking a bow and then walking into the darkness of the Petalburg Woods.

"Sapphire...something's bothering you." I said with concern in my voice.

"You see...Ruby's missing. He went out searching the man you just saw...it's been three weeks and no contact." She said, lowering her voice.

"Have you tried his PokéNav?" Joshua asked curiously.

"Yeah...I get a dial tone." Sapphire explained.

Where could he be? He couldn't have left Hoenn...

"Sapphire." I said, placing my arms on her shoulders. "Josh and I are gonna find Ruby." I assured her.

"Thank you, Aaron. You too, Joshua. Go on to Littleroot Town. I'll see the both of you when you return from Professor Birch's lab."

"Alright!" The both of us agreed, walking towards the Pokémon Center.

And in the morning, we were off on our way to Oldale Town.

Shoal Cave (?)

"Hm. The boy went looking for G, and all he found was trouble." A woman stated.

"Ugh...untie me!" Ruby demanded.

"Tell me who has the Mewtwo." The woman demanded.

"Ask G, since he knows everything!" Ruby replied cockily.

The woman growled. "Such insolence...you there, cover his mouth." She ordered a Grunt.

"Yes ma'm!" The Grunt agreed, walking towards Ruby, taping his mouth. He mumbled sounds.

"_Now with him in our grasp, those fools at Team Magma will have to hunt for him." _The woman thought.


End file.
